Variant rs2303611 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_032182.4(ABRAXAS2):c.606G>A(p.Val202=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 1,605,338 control chromosomes in the GnomAD database, including 259,381 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.48 ( 19927 hom., cov: 32)

Exomes 𝑓: 0.57 ( 239454 hom. )

Consequence

ABRAXAS2
NM_032182.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.00

Variant links:

Genes affected

ABRAXAS2 (HGNC:28975): (abraxas 2, BRISC complex subunit) Enables microtubule binding activity and polyubiquitin modification-dependent protein binding activity. Involved in several processes, including mitotic spindle assembly; protein K63-linked deubiquitination; and response to ischemia. Located in cytoplasm. Part of BRISC complex. Colocalizes with microtubule minus-end; midbody; and spindle pole centrosome. [provided by Alliance of Genome Resources, Apr 2022]

ABRAXAS2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP7

Synonymous conserved (PhyloP=-1 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ABRAXAS2	NM_032182.4 linkuse as main transcript	c.606G>A	p.Val202=	synonymous_variant	7/9	ENST00000298492.6	NP_115558.3
ABRAXAS2	XM_047424888.1 linkuse as main transcript	c.294G>A	p.Val98=	synonymous_variant	6/8		XP_047280844.1
ABRAXAS2	XM_047424889.1 linkuse as main transcript	c.294G>A	p.Val98=	synonymous_variant	4/6		XP_047280845.1
ABRAXAS2	XM_047424891.1 linkuse as main transcript	c.294G>A	p.Val98=	synonymous_variant	4/6		XP_047280847.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABRAXAS2	ENST00000298492.6 linkuse as main transcript	c.606G>A	p.Val202=	synonymous_variant	7/9	1	NM_032182.4	ENSP00000298492	P1

Frequencies

GnomAD3 genomes

AF:

0.485

AC:

73641

AN:

151930

Hom.:

19907

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.356

Gnomad AMR

AF:

0.596

Gnomad ASJ

AF:

0.645

Gnomad EAS

AF:

0.596

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.603

Gnomad MID

AF:

0.548

Gnomad NFE

AF:

0.573

Gnomad OTH

AF:

0.502

GnomAD3 exomes

AF:

0.564

AC:

140636

AN:

249308

Hom.:

41079

AF XY:

0.571

AC XY:

76982

AN XY:

134840

show subpopulations

Gnomad AFR exome

AF:

0.217

Gnomad AMR exome

AF:

0.611

Gnomad ASJ exome

AF:

0.668

Gnomad EAS exome

AF:

0.591

Gnomad SAS exome

AF:

0.618

Gnomad FIN exome

AF:

0.605

Gnomad NFE exome

AF:

0.564

Gnomad OTH exome

AF:

0.565

GnomAD4 exome

AF:

0.569

AC:

827324

AN:

1453290

Hom.:

239454

Cov.:

AF XY:

0.571

AC XY:

413198

AN XY:

723318

show subpopulations

Gnomad4 AFR exome

AF:

0.205

Gnomad4 AMR exome

AF:

0.609

Gnomad4 ASJ exome

AF:

0.663

Gnomad4 EAS exome

AF:

0.628

Gnomad4 SAS exome

AF:

0.613

Gnomad4 FIN exome

AF:

0.598

Gnomad4 NFE exome

AF:

0.570

Gnomad4 OTH exome

AF:

0.555

GnomAD4 genome

AF:

0.485

AC:

73679

AN:

152048

Hom.:

19927

Cov.:

AF XY:

0.493

AC XY:

36604

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.224

Gnomad4 AMR

AF:

0.596

Gnomad4 ASJ

AF:

0.645

Gnomad4 EAS

AF:

0.596

Gnomad4 SAS

AF:

0.642

Gnomad4 FIN

AF:

0.603

Gnomad4 NFE

AF:

0.573

Gnomad4 OTH

AF:

0.508

Alfa

AF:

0.549

Hom.:

30004

Bravo

AF:

0.470

Asia WGS

AF:

0.593

AC:

2058

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.84

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over